variantcomposition/.github/workflows/nf-test.yml at ba873c2c7b7c8abdb3e985ecc54b5a6a2375dc49 · sanger-tol/variantcomposition · GitHub

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name: Run nf-test
on:
  push:
    paths-ignore:
      - "docs/**"
      - "**/meta.yml"
      - "**/*.md"
      - "**/*.png"
      - "**/*.svg"
  pull_request:
    paths-ignore:
      - "docs/**"
      - "**/meta.yml"
      - "**/*.md"
      - "**/*.png"
      - "**/*.svg"
  release:
    types: [published]
  workflow_dispatch:

# Cancel if a newer run is started
concurrency:
  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

env:
  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
  NFT_VER: "0.9.2"
  NFT_WORKDIR: "~"
  NXF_ANSI_LOG: false
  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity

jobs:
  nf-test-changes:
    name: nf-test-changes
    runs-on: # use GitHub runners
      - "ubuntu-latest"
    outputs:
      shard: ${{ steps.set-shards.outputs.shard }}
      total_shards: ${{ steps.set-shards.outputs.total_shards }}
    steps:
      - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
        run: |
          ls -la ./
          rm -rf ./* || true
          rm -rf ./.??* || true
          ls -la ./
      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
        with:
          fetch-depth: 0

      - name: get number of shards
        id: set-shards
        uses: ./.github/actions/get-shards
        env:
          NFT_VER: ${{ env.NFT_VER }}
        with:
          max_shards: 7

      - name: debug
        run: |
          echo ${{ steps.set-shards.outputs.shard }}
          echo ${{ steps.set-shards.outputs.total_shards }}

  nf-test:
    name: "${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/${{ needs.nf-test-changes.outputs.total_shards }}"
    needs: [nf-test-changes]
    if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}
    runs-on: # use GitHub runners
      - "ubuntu-latest"
    strategy:
      fail-fast: false
      matrix:
        shard: ${{ fromJson(needs.nf-test-changes.outputs.shard) }}
        profile: [conda, docker, singularity]
        isMain:
          - ${{ github.base_ref == 'main' }}
        # Exclude conda and singularity on dev
        exclude:
          - isMain: false
            profile: "conda"
          - isMain: false
            profile: "singularity"
        NXF_VER:
          - "24.04.2"
          - "latest-everything"
    env:
      NXF_ANSI_LOG: false
      TOTAL_SHARDS: ${{ needs.nf-test-changes.outputs.total_shards }}

    steps:
      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
        with:
          fetch-depth: 0

      - name: Run nf-test
        uses: ./.github/actions/nf-test
        env:
          NFT_DIFF: ${{ env.NFT_DIFF }}
          NFT_DIFF_ARGS: ${{ env.NFT_DIFF_ARGS }}
          NFT_WORKDIR: ${{ env.NFT_WORKDIR }}
        with:
          profile: ${{ matrix.profile }}
          shard: ${{ matrix.shard }}
          total_shards: ${{ env.TOTAL_SHARDS }}
  confirm-pass:
    needs: [nf-test]
    if: always()
    runs-on: # use GitHub runners
      - "ubuntu-latest"
    steps:
      - name: One or more tests failed
        if: ${{ contains(needs.*.result, 'failure') }}
        run: exit 1

      - name: One or more tests cancelled
        if: ${{ contains(needs.*.result, 'cancelled') }}
        run: exit 1

      - name: All tests ok
        if: ${{ contains(needs.*.result, 'success') }}
        run: exit 0

      - name: debug-print
        if: always()
        run: |
          echo "::group::DEBUG: `needs` Contents"
          echo "DEBUG: toJSON(needs) = ${{ toJSON(needs) }}"
          echo "DEBUG: toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}"
          echo "::endgroup::"

      - name: Clean Workspace # Purge the workspace in case it's running on a self-hosted runner
        if: always()
        run: |
          ls -la ./
          rm -rf ./* || true
          rm -rf ./.??* || true
          ls -la ./